Homeopathy has become the focus of increasing interest and use as a complementary and alternative treatment for both human and animal disease. However, from the point of view of academic medicine, this type of therapy is controversial. The use of highly diluted remedies cannot be reconciled with the scientific theories on which the current understanding of disease and its treatment is based, and clinical research in the field is considered to be neither extensive enough nor of a high enough standard to determine whether homeopathic treatments are clinically effective. Animals have no choice in their treatment and are dependent on the judgements of their owners and their therapists. There is therefore a need for information about the effects and consequences of the use of alternative therapies. This paper discusses the use of homeopathy in the treatment of animal disease from the point of view of academic veterinary medicine, and the various approaches to research in this field, with an emphasis on the randomised clinical trial. It also discusses the role of the placebo response and the natural resolution of disease in the clinical evaluation of homeopathic treatment.